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As I write, the city of Maaloula in Syria has become a ghost town after being briefly occupied by members of the al Qaeda–linked jihadist group al-Nusra Front. Conflicting reports claim that al-Nusra fighters have desecrated churches and statues in what may be one of the oldest Christian cities in the world, a place where residents still speak Aramaic, the language presumably spoken by Jesus.

Sadly, the experience of Maaloula’s residents is becoming all too common in the Middle East, where examples of brutality against Christians have been mounting in recent weeks. In Egypt, the coup against President Mohamed Morsi was followed by a wave of Islamist pogroms against Christians in which 42 churches were attacked, 37 were burned or looted, and an untold number of Christians were assaulted or killed.

As tempting as it may be to attribute these events to the atmosphere of post-insurrectionary anarchy in Egypt and Syria, that is not the best vantage point from which to view the problem. Take a step back, and it becomes clear that the recent assaults are part of a bigger offensive against Middle Eastern Christians, one that can be traced back to decades-long developments in regional politics and Islamic society. The Arab Spring may be the proximate cause of some of the worst violence, but its roots run much deeper -- and the stakes are much higher than one might think. What we are witnessing is nothing less than a regional religious cleansing that will soon prove to be a historic disaster for Christians and Muslims alike.

At the start of World War I, the Christian population of the Middle East may have been as high as 20 percent. Today, it is roughly four percent. Although it is difficult to be exact, there are perhaps 13 million Christians left in the region, and that number has likely fallen further, given the continued destabilization of Syria and Egypt, two nations with historically large Christian populations. At the present rate of decline, there may very well be no significant Christian presence in the Middle East in another generation or two.

This would be a profoundly important loss. Christianity was born in the Middle East and had a deep, penetrating presence in the region for hundreds of years before the rise of Islam. In the fourth and fifth centuries, when tens of thousands of heterodox Christians were forced to flee a Roman Empire that considered them heretics, the lands of the Middle East and North Africa became a haven for them. In the years thereafter, the region became the epicenter of Christian theology. In the Arabian peninsula, a large, thriving Christian population played a pivotal role in influencing the early theological and political development of Islam. During the Inquisition (the twelfth to fourteenth centuries), Christian sectarians found refuge under Islamic rule, which classed all Christians, regardless of their doctrinal differences, as “people of the Book” and accorded them protected, albeit inferior, societal status.

The situation for Middle Eastern Christians changed dramatically in the colonial era. Because the colonial experiment was also an unapologetically Christianizing mission, one that overtly privileged indigenous Christians over Muslims and framed Islam as a backward culture in need of civilization, political tensions between the two communities erupted throughout the Middle East. Muslims tended to view their Christian neighbors as complicit in colonial oppression; indigenous Christians became the target of anticolonial backlash.

With the end of colonial rule in the twentieth century, the governments of the Middle East’s newly independent nation-states actively encouraged the exodus of their Christian citizens from the region by enacting laws limiting their rights to proselytize or build places of worship. The lot of the Christians who remained in the region worsened with the rise of political Islam in the 1950s and ’60s, as groups such as the Muslim Brotherhood encouraged Middle Eastern Muslims to think of nationalism and citizenship strictly through the lens of Islamic identity. The irony was that, at the same time, the secular authoritarian regimes in the Middle East burnished their reputations in the West by presenting themselves as protecting Christian minorities from Islamist fanatics.

The ascension of transnational jihadism over the last two decades raised the campaign against Christians to a fever pitch. Jihadist groups such as al Qaeda have been remarkably successful at framing conflicts as an all-out war between Christianity and Islam. Many of the region’s Muslims, even those who do not support al Qaeda, now profess to believe that Middle Eastern Christians are firmly aligned either with the “crusading” West (as in Iraq) or the “godless” tyrants and dictators (as in Syria and Egypt).

For example, the U.S. invasion of Iraq was widely portrayed as part of a Christian crusade against Islam; radical Muslims consistently (and successfully) argued that the country’s Christians were colluding with the U.S. military. The result is that at least 60 Christian churches have been attacked and more than a thousand Christians have been killed since the toppling of Saddam Hussein. By some estimates, nearly two-thirds of Iraq’s 1.5 million Christians have been forced to flee the country over the last ten years, many to Syria, where they found themselves once again under attack.

Syria’s Christian population has dropped from 30 percent in the 1920s to less than ten percent today. Although this mass exodus has been made worse by the civil war, its real cause lies in the decades-long psychological shift that occurred throughout the region as Christians became identified as enemies.Still, because so many Syrian Christians have been vocal supporters of the Assad regime -- either because their fortunes are tied to the government or because they fear the persecution that may follow if it falls -- it has been easy for the Syrian opposition to portray the country’s Christians as de facto collaborators with a brutal regime responsible for the mass murder of its own citizens. Since the start of the civil war, more than 40 churches have been damaged or destroyed, over a thousand Christians killed, and hundreds of thousands of Christians displaced.

A similar dynamic has been at work in Egypt, which boasts the oldest and largest Christian population in the Middle East. (Copts make up roughly ten percent of the population, or about eight million people.) Many Egyptian Christians, including the Coptic Pope Tawadros II, have made no secret of their support for the military coup that removed the democratically elected, Muslim Brotherhood–backed president from office. That support has opened the floodgates of unspeakable acts of violence by some supporters of the Muslim Brotherhood against the country’s Christian minority. Although Islamists have been at the forefront of this violence, they are not the only ones responsible. The police and military did little or nothing to prevent the attacks on Christians; Human Rights Watch went so far as to suggest that the government’s lack of response was meant to embolden and even encourage these acts of terror.

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Indeed, one should not forget that Egypt’s secular regimes have a history of targeting the country’s vulnerable Coptic population. Some of the most oppressive years for Christians were during Hosni Mubarak’s rule in the 1990s. Until the recent wave of violence, the worst massacre of Copts in post-revolutionary Egypt came at the hands of the very military many Copts now support. The Maspero massacre of October 2011, in which the Egyptian army deliberately stirred up anti-Coptic sentiment, left 26 Copts dead.

The tragedy for Christians in the region is obvious. They are losing their lives, their homes, and their houses of worship. They are being driven from their ancestral homelands and forced to flee as refugees to neighboring countries where they are, in many cases, equally unwelcome.

But it is important to note that the removal of the region’s Christians is a disaster for Muslims as well. They are the ones who will be left with the task of building decent societies in the aftermath of these atrocities. And that task will be made immeasurably harder by the removal of Christians from their midst. It is not just that the memory of these brutal actions will taint these societies -- perpetrators and victims alike -- for the indefinite future; it is also that Muslims are removing the sort of pluralism that is the foundation for any truly democratic public life. One of the refrains of the Arab Spring has been that Muslims want to put an end to tyranny. But the only lasting guarantor of political rights is the sort of social and religious diversity that Muslims in the region are in the process of extinguishing. If nothing is done to reverse the situation, the hope for peace and prosperity in the Middle East may vanish along with the region’s Christian population.